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Hydrogen Bonding (0):
Recent article
Hydrogen Bonding
Abstract
Two new crystal structures, calcium bis(hydrogen methylphosphonate), Ca(CH(3)PO(3)H)(2), and lithium hydrogen methylphosphonate, Li(CH(3)PO(3)H), have been obtained, and the experimental and theoretical charge densities, as well as their topological properties, are reported. Both compounds display la...
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PMID: 21931209
PDF is available here.
PDF is available here.
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Abstract
O(6)-methylguanine (O(6)-MeG) is a miscoding DNA lesion arising from the alkylation of guanine. This report uses the bacteriophage T4 DNA polymerase as a model to probe the roles of hydrogen-bonding interactions, shape/size, and nucleobase desolvation during the replication of this miscoding lesion....
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PMID: 21819995
PDF is available here.
PDF is available here.
Abstract
We use Φ-value and double mutant analyses to probe the folding transition state of the membrane protein bacteriorhodopsin. We focus on the final C-terminal helix, helix G, of this seven transmembrane helical protein. Φ-values could be derived for 12 amino acid residues in helix G, most of which ha...
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PMID: 21831834
PDF is available here.
PDF is available here.
Abstract
Photophysical properties of a natural plant alkaloid, ellipticine (5,11-dimethyl-6H-pyrido[4,3-b]carbazole), which comprises both proton donating and accepting sites, have been studied in different solvents using steady state and time-resolved fluorescence techniques primarily to understand the origi...
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PMID: 21812494
PDF is available here.
PDF is available here.
Abstract
We report the crystal structure of a motor domain dimer in complex with its tail domain at 2.2 angstroms and compare it with a structure of the motor domain alone at 2.7 angstroms. These structures indicate that neither an induced conformational change nor steric blocking is the cause of inhibition....
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PMID: 21836017
PDF is available here.
PDF is available here.
Ukrainskij biokhimicheskij zhurnal/Ukrayins'kij biokhimichnij zhurnal/Ukrainian biochemical journal (82)6 2011
Abstract
The conformational analysis of the DNA structural unit--the nucleotide with thymine base and electroneutral phosphate group at 5'-position-has been carried out with the applied quantum mechanics methods at the MP2/6-311++G(d,p) // B3LYP/6-31G(d,p) theory level. As many as 660 conformations with relat...
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PMID: 21805865
PDF is available here.
PDF is available here.
Abstract
Our findings are in accordance with previously reported results obtained from the kinetic studies of the binding of acridine and related tricyclic carboxamides to DNA....
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PMID: 21153908
PDF is available here.
PDF is available here.
Abstract
The partial modification of carboxylic acid terminated polyamidoamine (PAMAM) dendrimers with glucosamine has been reported to give dendrimer glucosamine conjugates novel immuno-modulatory and anti-angiogenic properties. Experimental analysis of these glycosylated dendrimers showed t...
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PMID: 21161557
PDF is available here.
PDF is available here.
Abstract
The reaction of cyclopropanes, geminally disubstituted with one carboalkoxy and one carbohydroxy group, undergoes ring-opening reactions with indole nucleophiles under catalyst-free, hyperbaric (13 kbar) conditions. An internal hydrogen bond is postulated as the mode of activation ob...
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PMID: 21766828
PDF is available here.
PDF is available here.
Abstract
A neutral ferrocene-appended aryl triazole receptor 1 for phosphate anions has been synthesized and characterized by X-ray crystal analysis. Among various anions, 1 shows a distinct electrochemical recognition of phosphate anions by its multiple H-bonding (C-H···O) with a tetrahed...
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PMID: 21774510
PDF is available here.
PDF is available here.
Abstract
We investigated an Austrian family with 16 affected individuals by exome sequencing. We found a missense mutation, c.1858G>A (p.Asp620Asn), in the VPS35 gene in all seven affected family members who are alive. By screening additional PD cases, we saw the same variant cosegregating with the disease i...
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PMID: 21763483
PDF is available here.
PDF is available here.
Abstract
A hydrogen-bond-assisted model is proposed for ring-opening metathesis polymerization (ROMP) of a secondary amide of 1-cyclobutene, resulting in the fastest reaction rate in a nonpolar solvent, toluene. This new model was supported by the investigation on how the solvent effect affec...
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PMID: 21740018
PDF is available here.
PDF is available here.
Abstract
We performed multiple molecular dynamics simulations of the mutated A-site RNA fragment in explicit solvent to analyze changes in the physicochemical features of the A-site that were introduced by substitutions of specific bases. The simulations were conducted for free RNA and in complex with paromo...
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PMID: 21814503
PDF is available here.
PDF is available here.
Abstract
A facile strategy to perform the boron coordination reaction on a template of nanofibers is developed. Peptides with phenylboronic acid tails (peptidyl boronic acids) are designed and prepared as building blocks that can self-assemble into nanofibers. After the addition of vicinal di...
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PMID: 21728226
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)7 2011
Abstract
We present the solution structure of GIP in membrane-mimicking environments by proton NMR spectroscopy and molecular modelling. GIP adopts an α-helical conformation between residues Phe(6)-Gly(31) and Ala(13)-Gln(29) for micellar and bicellar media, respectively. Previously we examined the effect o...
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PMID: 21539943
PDF is available here.
PDF is available here.
Abstract
Base pairs formed by the inosine nucleoside (I) play an important role in many physiological processes as well as in various DNA technologies. Relative stabilities and favored base pair geometries of free inosine wobble base pairs in aprotic solvents have been determined through (1)H NMR measurements...
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PMID: 21644523
PDF is available here.
PDF is available here.
Abstract
The conformational space of 1H-Indole-3-Acetic Acid (IAA) was scanned using molecular dynamics at semiempirical level, and complemented with functional density calculations at B3LYP/6-31G** level, 14 conformers of lowest energy were obtained. Electronic distributions were analyzed at...
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PMID: 20706854
PDF is available here.
PDF is available here.
Abstract
The mechanism of phenylselenoetherification of pent-4-en-1-ol using some bases (pyridine, triethylamine, quinoline, 2,2'-bipyridine) as catalyst was examined through studies of kinetics of the cyclization, by UV-VIS spectrophotometry. It was demonstrated that the intramolecular cycli...
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PMID: 20711793
PDF is available here.
PDF is available here.
Abstract
Topological analysis based on DFT calculations regarding proton transfer reaction in salicylideneaniline (SA) was performed to scrutinize possible changes in the intramolecular H-bond, pi-electron delocalization and aromaticity levels of certain fragments. Quantum chemical calculatio...
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PMID: 20820826
PDF is available here.
PDF is available here.
Abstract
Interleukin-1beta (IL-1beta) is an important cytokine in the immune system. Mammalian and avian IL-1betas share only 31-35% sequence identity, and the function of avian IL-1betas is less well understood by comparison. Although chicken and mammalian IL-1betas have similar tertiary str...
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PMID: 20820827
PDF is available here.
PDF is available here.
Abstract
Quantum chemical methods have been used to study the conformational and electronic properties of sulfanilamide and derivatives with antibacterial activity. Calculations at B3LYP/6-311++G(3df,2p) level of theory predict the existence of four conformers for sulfanilamide depending on t...
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PMID: 20820828
PDF is available here.
PDF is available here.
Abstract
Our analysis showed that dimeric forms predicted theoretically contribute distinctively to the assignments of experimental results. These structures are defined by the orientation of the acetyl moieties with respect to the plane of indole ring. The dimers are formed by two symmetrical IAA monomers (...
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PMID: 20839020
PDF is available here.
PDF is available here.
Abstract
The formation of α-turns is a possibility to reverse the direction of peptide sequences via five amino acids. In this paper, a systematic conformational analysis was performed to find the possible isolated α-turns with a hydrogen bond between the first and fifth amino acid employin...
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PMID: 20842396
PDF is available here.
PDF is available here.
Abstract
We have characterized the binding properties between sialic acid, methyl 3'sialyllactoside, methyl 6'sialyllactoside and the H5N1 influenza virus neuraminidase using molecular docking and molecular dynamics simulations. Obtained molecular dynamics trajectories were analyzed in terms of ligand confor...
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PMID: 20853123
PDF is available here.
PDF is available here.
Abstract
We theoretically discuss the relationship between diffusivity and hydrated structures of DNA fragments in water solvent using molecular dynamics methods. In particular, influence of base pair substitutions on the diffusivity is investigated, focusing on an adenine-thymine (AT) rich B-DNA decamer 5'-...
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PMID: 20853125
PDF is available here.
PDF is available here.
Abstract
Density functional theoretical calculations have been utilized to investigate the interaction of the amino acid arginine with the (100) surface of anatase and the reproduction of experimentally measured (49)Ti NMR chemical shifts of anatase. Significant binding of arginine through el...
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PMID: 20853182
PDF is available here.
PDF is available here.
Abstract
Enoyl-acyl carrier protein (ACP) reductase (ENR) is an attractive and potential target for developing selective antibacterial agents. Recent studies showed that FabK is the sole isoform of ENR in Streptococcus pneumoniae, and at the same time an X-ray crystallographic study of FabK f...
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PMID: 20862594
PDF is available here.
PDF is available here.
Abstract
A homology model for pig liver esterase was generated on the basis of human carboxyl esterase (hCE) and subjected to extensive molecular dynamics simulations. By virtual mutations the isoenzymes PLE1-6 and APLE were obtained, and the PLE1 trimer was built from the respective model of...
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PMID: 20862595
PDF is available here.
PDF is available here.
Abstract
Our simulations suggest the mechanism of acid-induced apatite decomposition to i) require a considerable degree of protonation of the apatite surface. The first ion dissociation step ii) involves calcium ions which electrostatic binding has been locally destabilized through phosphate and hydroxide p...
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PMID: 20886246
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1814)6 2011
Abstract
We present the first structural characterization of a group II 2/2Hb from the soil and phytopathogenic bacterium Agrobacterium tumefaciens (At-2/2HbO). The crystal structure of ferric At-2/2HbO (reported at 2.1 Å resolution) shows the location of specific/unique heme distal site residues (e.g. His(...
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PMID: 21070893
PDF is available here.
PDF is available here.
Abstract
Water-binding foldamers have been rarely studied. By orienting both H-bond donors and acceptors toward their interior, two pyridine-derived crescent-shaped folding oligoamides were found to be capable of trapping both conventional and unconventional water dimer clusters in their cavi...
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PMID: 21591725
PDF is available here.
PDF is available here.
Abstract
We found several well-known inactive Zf cores containing Cys ligands with no H-bonding interactions. Here, we show that H bonds from the peptide backbone or bonds from a second Zn cation to Zn-bound S atoms suppress the reactivity not only of these S atoms, but also of Zn-bound S* atoms with no inte...
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PMID: 21574548
PDF is available here.
PDF is available here.
Abstract
We are developing solid-state NMR (SSNMR) to probe the flavin electronic structure, via the (15)N chemical shift tensor principal values (δ(ii)). We find that SSNMR has superior responsiveness to H-bonds, compared to solution NMR. H-bonding to a model of the flavodoxin active site produced an incre...
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PMID: 21619002
PDF is available here.
PDF is available here.
Abstract
Our approach provides an explanation of the experimental difficulty of observing the reentrant transition with pressure and underscores the advantage of pulling experiments for studies of DNA. Results are discussed and compared with those reported in a number of recent publications with which a sign...
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PMID: 21728568
PDF is available here.
PDF is available here.
Abstract
Combined low-temperature NMR/UV-vis spectroscopy (UVNMR), where optical and NMR spectra are measured in the NMR spectrometer under the same conditions, has been set up and applied to the study of H-bonded anions A··H··X(-) (AH = 1-(13)C-2-chloro-4-nitrophenol, X(-) = 15 carboxylic acid anions, 5...
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PMID: 21534587
PDF is available here.
PDF is available here.
Abstract
We present what we believe to be a novel procedure, based on combinations of multistep trajectories, that was used to estimate the binding free energy (ΔG) of each disaccharide. The computed binding free energy differences show excellent correlation with experimental values determined previously. T...
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PMID: 21539798
PDF is available here.
PDF is available here.
Abstract
We used atomistic molecular-dynamics simulation to examine the thermodynamic stability of a amyloid fibrils in different polymorphic forms by performing a systematic investigation of sequence and symmetry space for a series of peptides with a range of physicochemical properties. We show that the sta...
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PMID: 21539792
PDF is available here.
PDF is available here.
Abstract
We review and compare the structural differences in the vicinity of the active sites of these enzymes and discuss which changes could give rise to the different behavior of H(peroxo) and Q. In particular, analysis of multiple crystal structures reveals that T213 in MMOH and the analogous T201 in TMO...
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PMID: 21517016
PDF is available here.
PDF is available here.
Abstract
A heme model system has been developed in which the heme-propionate is the only proton donating/accepting site, using protoporphyrin IX-monomethyl esters (PPIX(MME)) and N-methylimidazole (MeIm). Proton-coupled electron transfer (PCET) reactions of these model compounds have been examined in acetonit...
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PMID: 21524059
PDF is available here.
PDF is available here.
Abstract
We present a series of high-resolution (1.15-1.80 Å) crystal structures of a fluoroacetate dehalogenase, capturing snapshots along the defluorination reaction: the free enzyme, enzyme-fluoroacetate Michaelis complex, glycolyl-enzyme covalent intermediate, and enzyme-product complex. We demonstrate...
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PMID: 21510690
PDF is available here.
PDF is available here.
Abstract
We have investigated the mutation effects on the structures and thermodynamics for the aggregation and folding of AcP by using the combination of fully atomistic, explicit-water molecular dynamics simulations, and three-dimensional reference interaction site model theory. The results indicate that t...
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PMID: 21500781
PDF is available here.
PDF is available here.
Abstract
A new functional bifacial nucleoside derived from 7-aminopyrimido[4,5-d]pyrimidine-2,4(1H,3H)-dione, a Janus-type nucleobase, has been synthesized and incorporated into DNA oligonucleotides. The nucleobase, having self-complementary H-bonding faces, mimics both T and A and engages in the correspondin...
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PMID: 21495708
PDF is available here.
PDF is available here.
Abstract
Our results reveal also the existence of two regimes, suggesting the presence of multiple energy barriers in the energy landscape. From these dynamic force spectroscopy measurements, the kinetic off-rate constant is determined. An average unbinding force in the range of 50-300 pN is obtained, depend...
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PMID: 21488141
PDF is available here.
PDF is available here.
Abstract
We have conducted studies on the drug resistance through docking and binding analysis supported by time-scale (∼ 1000 ps) and unrestrained all-atom molecular dynamics simulations of wild and mutant MtBKatG. The study showed conformational changes of binding residues. Mutant (S315T) showed high doc...
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PMID: 20593210
PDF is available here.
PDF is available here.
Abstract
We investigated the mechanism that enables paullones to selectively inhibit GSK-3 rather than cyclin-dependent kinase 5 (CDK5) using sequence alignment, molecular dynamics simulations, free-energy calculations and free-energy decomposition analysis. The results indicate that the interaction between...
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PMID: 20559856
PDF is available here.
PDF is available here.
Abstract
We investigated the mechanism that enables paullones to selectively inhibit GSK-3 rather than cyclin-dependent kinase 5 (CDK5) using sequence alignment, molecular dynamics simulations, free-energy calculations and free-energy decomposition analysis. The results indicate that the interaction between...
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PMID: 20559856
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)8 2011
Abstract
We investigate the interactions of C6-LfB6, N-acylated with a 6 carbon fatty acid, with model lipid bilayers with two distinct compositions: 3:1 POPE:POPG (negatively charged) and POPC (zwitterionic). Results from solid-state (2)H and (31)P NMR experiments are compared with those from an ensemble of...
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PMID: 21477580
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)8 2011
Abstract
We previously tested this hypothesis in lipid bilayers and showed that the mutation stabilizes the isolated transmembrane domain dimer by -1.3°kcal/mol. Here we further test the hypothesis, by investigating the effect of the A391E mutation on the activation of full-length fibroblast growth factor r...
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PMID: 21536014
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)9 2011
Abstract
The positively charged side chains of cationic antimicrobial peptides are generally thought to provide the initial long-range electrostatic attractive forces that guide them towards the negatively charged bacterial membranes. Peptide analogs were designed to examine the role of the four Arg side chai...
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PMID: 21641334
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)9 2011
Abstract
We studied the conformation of SRE bound to SDS micelle, a suitable model for the membrane-bound SRE. In fact, highly similar circular dichroism (CD) spectra were obtained for SRE bound to sodium dodecylsulphate (SDS) and to a phospholipid bilayer, indicating the conformational equivalence of SRE in...
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PMID: 21658366
PDF is available here.
PDF is available here.
Abstract
We have studied by rapid scan FTIR spectroscopy the isothermal B(I)-B(II) transition on its intrinsic time scale. Correlation analysis of IR absorption changes occurring within seconds after a reversible incremental growth of the DNA hydration shell identifies water populations w(1) (PO(2)(-)-bound)...
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PMID: 21446714
PDF is available here.
PDF is available here.
Abstract
The intermolecular interactions of the photodamaged cyclobutane pyrimidine dimer (CPD) lesion with adjacent nucleobases in the native intrahelical DNA double strand are investigated at the level of density functional theory symmetry-adapted perturbation theory (DFT-SAPT) and compared to the original...
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PMID: 21452189
PDF is available here.
PDF is available here.
Abstract
We show that it is possible to fabricate the nanodroplets by assembling highly deformable nanogels into the nanoscale suprastructures at spatially confined O/W interfaces. The compressed assembly of the nanogels induced the formation of the nanoscale suprastructures upon the energy input at the nano...
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PMID: 21375220
PDF is available here.
PDF is available here.
Abstract
We have applied X-band HYSCORE, a 2D pulsed EPR technique, to characterize the exchangeable protons around the semiquinone (SQ) in the Q(A) and Q(B) sites, using samples of (15)N-labeled reaction centers, with the native high spin Fe(2+) exchanged for diamagnetic Zn(2+), prepared in (1)H(2)O and (2)...
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PMID: 21417328
PDF is available here.
PDF is available here.
Abstract
Molecular dynamics simulations were used to study the interactions of three theaflavin compounds with lipid bilayers. Experimental studies have linked theaflavins to beneficial health effects, some of which are related to interactions with the cell membrane. The molecular interaction of theaflavins w...
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PMID: 21417313
PDF is available here.
PDF is available here.
Abstract
These results can be related to the density of water molecules around the biological interface, suggesting that the apparent local density of water is larger in a hydrophilic environment....
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PMID: 21405120
PDF is available here.
PDF is available here.
Abstract
We report the synthesis, physical properties, and catalytic activity of a water-soluble segmented terpolymer in which a helical structure in the apolar core is created around a ruthenium-based catalyst. The supramolecular chirality of this catalytic system is the result of the self-assembly of benze...
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PMID: 21405022
PDF is available here.
PDF is available here.
Abstract
Ensemble infrared photodissociation (IRPD) spectra in the hydrogen stretch region (∼2950-3800 cm(-1)) are reported for M(H(2)O)(35-37), with M = I(-), Cl(-), HCO(3)(-), OH(-), tetrabutyl-, tetrapropyl-, and tetramethylammonium, Cs(+), Na(+), Li(+), H(+), Ba(2+), Ca(2+), Co(2+), Mg(2+), La(3+), and...
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PMID: 21405134
PDF is available here.
PDF is available here.
Biochimica et Biophysica Acta (1808)8 2011
Abstract
We incorporate the electrostatic-hydrogen bond switch mechanism into the Gouy-Chapman model for a membrane that is composed of PA and a hydrogen bond-donating zwitterionic lipid. To this end, our model integrates into the Gouy-Chapman approach a recently suggested electrostatic model for zwitterioni...
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PMID: 21406179
PDF is available here.
PDF is available here.
Biopolymers (95)9 2011
Abstract
I collagen and pigskin dermis were performed to probe relative humidity (RH)-dependent differences in the nature and level of collagen hydration. Raman spectra were also acquired as a function of time for both Type I collagen and pigskin dermis samples upon exchange of a 100% RH H(2) O to deuterium...
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PMID: 21394716
PDF is available here.
PDF is available here.